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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Microbial Symbioses
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1405751
This article is part of the Research Topic Plant Microbiome: Interactions, Mechanisms of Action, and Applications, Volume III View all 9 articles

Global citrus root microbiota unravels assembly cues and core members

Provisionally accepted
Monia F. Lombardo Monia F. Lombardo 1Yunzeng Zhang Yunzeng Zhang 2Jin Xu Jin Xu 2PANKAJ TRIVEDI PANKAJ TRIVEDI 3Pengfan Zhang Pengfan Zhang 4Nadia Riera Nadia Riera 2Lei Li Lei Li 2Ya-Yu Wang Ya-Yu Wang 4XIN LIU XIN LIU 4Guangyi Fan Guangyi Fan 4Ji-Liang Tang Ji-Liang Tang 5Helvécio D. Coletta-Filho Helvécio D. Coletta-Filho 6Jaime Cubero Jaime Cubero 7Xiaoling Deng Xiaoling Deng 8Veronica Ancona Veronica Ancona 9Zhanjun Lu Zhanjun Lu 10Balian Zhong Balian Zhong 10Caroline Roper Caroline Roper 11Nieves Capote Nieves Capote 12Vittoria Catara Vittoria Catara 1Gerhard Pietersen Gerhard Pietersen 13Abdullah M. Al-Sadi Abdullah M. Al-Sadi 14Xun Xu Xun Xu 4Jian Wang Jian Wang 4Huanming Yang Huanming Yang 4Tao Jin Tao Jin 4Gabriella Cirvilleri Gabriella Cirvilleri 1Nian Wang Nian Wang 2*
  • 1 University of Catania, Catania, Sicily, Italy
  • 2 University of Florida, Gainesville, Florida, United States
  • 3 Colorado State University, Fort Collins, Colorado, United States
  • 4 Beijing Genomics Institute (BGI), Shenzhen, China
  • 5 Guangxi University, Nanning, Guangxi Zhuang Region, China
  • 6 Sylvio Moreira Citriculture Center, Cordeirópolis, Brazil
  • 7 Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Madrid, Spain
  • 8 South China Agricultural University, Guangzhou, Guangdong Province, China
  • 9 Texas A&M University Kingsville, Kingsville, Texas, United States
  • 10 Gannan Normal University, Ganzhou, Jiangxi Province, China
  • 11 University of California, Riverside, Riverside, California, United States
  • 12 IFAPA Centro Las Torres Tomejil, Sevilla, Spain
  • 13 Stellenbosch University, Stellenbosch, Western Cape, South Africa
  • 14 Sultan Qaboos University, Muscat, Oman

The final, formatted version of the article will be published soon.

    Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth. In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries encompassing all six continents. We analysed the 16S rDNA and ITS2 amplicon sequencing data. Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the root prokaryotic and fungal communities were less diverse and complex but more modular than the rhizosphere ones. 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. We have conducted citrus genotype-based group-wise comparisons which revealed that the citrus genotype had a significant impact on the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were also predicted. Overall, this study provides new information about assemblage of microbial communities and core members of citrus root microbiota in a broad biogeographical sampling. This study is valuable in manipulating the root microbiota for plant growth and health.

    Keywords: Endophytes, beneficial microorganisms, Core microbiome, Rootstock selection, Biological Control Agents

    Received: 23 Mar 2024; Accepted: 09 Jul 2024.

    Copyright: © 2024 Lombardo, Zhang, Xu, TRIVEDI, Zhang, Riera, Li, Wang, LIU, Fan, Tang, Coletta-Filho, Cubero, Deng, Ancona, Lu, Zhong, Roper, Capote, Catara, Pietersen, Al-Sadi, Xu, Wang, Yang, Jin, Cirvilleri and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Nian Wang, University of Florida, Gainesville, 32609, Florida, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.